Package: methylInheritance 1.31.0

Astrid Deschênes

methylInheritance: Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.

Authors:Astrid Deschênes [cre, aut], Pascal Belleau [aut], Arnaud Droit [aut]

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methylInheritance/json (API)
NEWS

# Install 'methylInheritance' in R:

install.packages('methylInheritance', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adeschen/methylinheritance/issues

Datasets:

demoForTransgenerationalAnalysis - The methylation information from samples over three generations. Information for each generation is stored in a 'methylRawList' format (for demo purpose).
methylInheritanceResults - All observed and permutation results formatted in a 'methylInheritanceResults' class (for demo purpose).
samplesForTransgenerationalAnalysis - All samples information, formated by 'methylKit', in a 'methylRawList' format (for demo purpose).

On BioConductor:methylInheritance-1.29.0(bioc 3.20)methylInheritance-1.28.0(bioc 3.19)

biologicalquestion epigenetics dnamethylation differentialmethylation methylseq software immunooncology statisticalmethod wholegenome sequencing analysis bioconductor bioinformatics cpg differentially-methylated-elements inheritance monte-carlo-sampling permutation

4.60 score 1 scripts 194 downloads 9 exports 103 dependencies

Last updated 23 days agofrom:9150e3e680. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	OK	Oct 31 2024

Exports:calculateSignificantLevel extractInfo loadAllRDSResults loadConvergenceData mergePermutationAndObservation plotConvergenceGraph plotGraph runObservation runPermutation

Dependencies:abind askpass bbmle bdsmatrix BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops cli coda codetools colorspace cpp11 crayon curl data.table DelayedArray emdbook fansi farver fastseg formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue gridExtra gtable gtools httr IRanges isoband jsonlite KernSmooth labeling lambda.r lattice lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats mclust methylKit mgcv mime munsell mvtnorm nlme numDeriv openssl pillar pkgconfig plyr qvalue R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl rebus rebus.base rebus.datetimes rebus.numbers rebus.unicode reshape2 restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors scales snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml zlibbioc

Inferring inheritance of differentially methylated changes across multiple generations

Astrid Deschênes, Pascal Belleau and Arnaud Droit

Rendered frommethylInheritance.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2018-11-30
Started: 2017-04-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
methylInheritance: Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment Effect	methylInheritance-package methylInheritance
Calculate significant level for hypo and hyper conserved elements	calculateSignificantLevel
The methylation information from samples over three generations. Information for each generation is stored in a 'methylRawList' format (for demo purpose).	demoForTransgenerationalAnalysis
Extract the information specific to a subsection of the permutation analysis	extractInfo
Load all RDS files created by the permutation and observation analysis	loadAllRDSResults
Load convergence information from RDS files	loadConvergenceData
Merge the permutation results with the observation results.	mergePermutationAndObservation
All observed and permutation results formatted in a 'methylInheritanceResults' class (for demo purpose).	methylInheritanceResults
Generate a graph showing the convergence for a permutation analysis	plotConvergenceGraph
Generate a graph for a permutation analysis	plotGraph
Print a 'methylInheritanceAllResults' object	print.methylInheritanceAllResults
Run a differential methylation analysis on multi-generational dataset	runObservation
Run all permutations on the specified multi-generational dataset	runPermutation
All samples information, formated by 'methylKit', in a 'methylRawList' format (for demo purpose).	samplesForTransgenerationalAnalysis